Nanoindentation offers a convenient method for the testing of thin hydrogel specimens, such as contact lenses, to directly assess their mechanical properties. Here we investigate the mechanical properties of poly(hydroxyethyl methacrylate) (pHEMA) specimens of a range of uniform thickness values and demonstrate that, with 50 and 100μm radius spherical indenters, a significant increase in apparent elastic modulus is seen when the specimen thickness is smaller than 500μm at indentation depths <1μm. This is a manifestation of the well known indentation thickness effect but occurring at larger critical thicknesses than seen with other materials. A simple empirical relation is determined for the variation in apparent elastic modulus with normalised thickness. The empirical thickness correction function obtained from pHEMA specimens was subsequently used to correct for the thickness variation within a range of contact lenses supplied by a number of different manufacturers fabricated from both pHEMA and silicone polymers, with a range of optical strengths and hence thickness profiles. The correction function is seen to compensate for the variation in apparent elastic modulus with lens thickness for all four contact lens types, irrespective of lens material. The measured Young's modulus of the contact lens material, corrected for thickness, was compared with that quoted by the manufacturers of the contact lenses, obtained by conventional bulk mechanical testing, to find good agreement.